What thermal paste did you use? How did you apply it?
Also running XTU whilst using TS is not gonna help much. The programs conflict with each other in some cases. And with XTU it will undervolt both CPU and cache together, which can cause instability, whereas with TS you can do them independently of each other. Stick with TS for your undervolt.
Defo look at how your cooler/pipes were seated. As
@hotaru.hino suggested if it's not flush with proper application of the paste, your CPU could very well spike that high under load. When screwing the heat pipes back down (and after you've done a new application of thermal paste) try criss crossing them. So if there are 4 screws tighten them at opposite corners diagonally, so it applies even pressure on the paste to spread out properly.
edit: Also, set your OSD in MSI to show the CPU clockspeed for all cores. It will provide a better idea of your CPU clockspeed changes and what throttling might be going on.
But your CPU temps at a consistent 96-99c range are worrying. Without a doubt it's throttling.
Is the laptop flat on your desk, or raised, or on a cooling pad? Airflow underneath will really help too.